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AGRIS specifications

Information


Unique identifier OMICS_00548
Name AGRIS
Alternative name Arabidopsis Gene Regulatory Information Server
Restrictions to use Academic or non-commercial use
Community driven No
Data access File download
User data submission Not allowed
Maintained Yes

Maintainers


  • person_outline Erich Grotewold
  • person_outline Alper Yilmaz

Publications for Arabidopsis Gene Regulatory Information Server

AGRIS citations

 (35)
library_books

Dietary species richness as a measure of food biodiversity and nutritional quality of diets

2017
Proc Natl Acad Sci U S A
PMCID: 5776793
PMID: 29255049
DOI: 10.1073/pnas.1709194115

[…] Existing data were first mapped using a systematic literature review (). The search syntax was applied to 10 databases: (i) Agricola, (ii) Agris, (iii) Bioline International, (iv) EMBASE, (v) IngentaConnect, (vi) Web of Knowledge, (vii) Medline (through PubMed), (viii) Science Direct, (ix) Cochrane Library of Systematic Reviews, and (x) […]

library_books

Transcriptome dynamics revealed by a gene expression atlas of the early Arabidopsis embryo

2017
PMCID: 5687563
PMID: 29116234
DOI: 10.1038/s41477-017-0035-3

[…] d to assess the FDR. GO terms with p ≤0.001 or FDR <0.05 were considered significantly enriched. Transcription factors (TFs) belonging to a family were identified using the Arabidopsis TF database at AGRIS. […]

library_books

Redundant CArG Box Cis motif Activity Mediates SHATTERPROOF2 Transcriptional Regulation during Arabidopsis thaliana Gynoecium Development

2017
Front Plant Sci
PMCID: 5650620
PMID: 29085379
DOI: 10.3389/fpls.2017.01712

[…] Binding sites from PLACE (), AGRIS () and TRANSFAC () databases were mapped to the SHP2 genomic locus including 3kb upstream of the SHP2 translation start site using PatMaN software (). Output results files from PatMaN were conve […]

call_split

Evolutionary relationships and expression analysis of EUL domain proteins in rice (Oryza sativa)

2017
PMCID: 5449364
PMID: 28560587
DOI: 10.1186/s12284-017-0164-3
call_split See protocol

[…] Cis-regulatory elements were obtained from AGRIS (Palaniswamy et al. ), PLACE (Higo et al. ), Athamap (Steffens et al. ), CisBP (Weirauch et al. ), JASPAR (Mathelier et al. ) and TRANSFAC (Matys et al. ). These elements were mapped to 2 kb ups […]

library_books

Integrated analysis of 454 and Illumina transcriptomic sequencing characterizes carbon flux and energy source for fatty acid synthesis in developing Lindera glauca fruits for woody biodiesel

2017
Biotechnol Biofuels
PMCID: 5445305
PMID: 28559925
DOI: 10.1186/s13068-017-0820-2

[…] oping L. glauca fruits.Fig. 6 Also of note was the involvement of transcription factors (TFs) in oil biosynthesis during fruit development of L. glauca. We analyzed all the unigenes by BLASTX against AGRIS database, and annotated TFs (ABI3, WRI1, LEC1, FUS3, HSI2, AP2, and GL2) in developing L. glauca fruits (Additional file : Table S11), which was known for the regulation of plant oil accumulatio […]

library_books

Differential Coexpression Analysis Reveals Extensive Rewiring of Arabidopsis Gene Coexpression in Response to Pseudomonas syringae Infection

2016
Sci Rep
PMCID: 5056366
PMID: 27721457
DOI: 10.1038/srep35064

[…] databases.After removing redundant interactions, we collected 50,824 TF-target binary interactions between 529 TFs and 22,793 target genes from the Arabidopsis Transcriptional Regulatory Map (ATRM), AGRIS and AthaMap (). In total, 13,879 interactions between 333 TFs and 5,371 targets were retained for further analysis by filtering out stably expressed genes under each condition (variance <0.2 in […]


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AGRIS institution(s)
Department of Plant Cellular and Molecular Biology and Plant Biotechnology Center, The Ohio State University, Columbus, OH, USA; School of Electrical Engineering and Computer Science, Ohio University, Athens, OH, USA
AGRIS funding source(s)
Supported by National Science Foundation (MCB-0418891); and National Institutes of Health (5 T32 CA106196-05).

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